phyloTop {phyloTop}

phyloTop: topological properties of phylogenies

Description

Calculate a range of topological properties for one or more phylogenetic trees.

Usage

phyloTop(treeList, funcs = "all", normalise = FALSE)

Arguments

treeList

a list or multiPhylo object, or a single tree of class phylo or phylo4. All trees should be binary and rooted; if not they will be coerced into binary rooted trees using multi2di, if possible.

funcs

a list of functions. The default is to apply all of the topological functions from the package, but a subset can be specified instead. The functions available are:

• avgLadder

• cherries

• colless.phylo

• ILnumber

• maxHeight

• pitchforks

• sackin.phylo

• stairs (note that this adds two columns to the output, "stairs1" and "stairs2")

normalise

option to normalise the results of functions where possible. Default is FALSE

Value

A matrix where rows correspond to trees and columns correspond to topological properties.

Author(s)

Michelle Kendall [e-mail]

See Also

avgLadder, cherries, colless.phylo, ILnumber, maxHeight, pitchforks, sackin.phylo, stairs

Examples

## Apply all of the functions to a list of 10 random trees, each with 50 tips:
phyloTop(rmtree(10,50))
## Normalising the results where possible:
phyloTop(rmtree(10,50), normalise=TRUE)